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Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses

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Abstract
The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders – Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.
Keywords
Siphonous green algae, Seaweeds, Chloroplast genome, Phylogeny, Ulvophyceae, UDOTEACEAE BRYOPSIDALES, GENUS, SELECTION, HALIMEDA, GENOME, AVRAINVILLEA, ULVOPHYCEAE, DIVERSITY, ALGORITHM, ALIGNMENT

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Citation

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MLA
Cremen, Ma Chiela M et al. “Reassessment of the Classification of Bryopsidales (Chlorophyta) Based on Chloroplast Phylogenomic Analyses.” MOLECULAR PHYLOGENETICS AND EVOLUTION 130 (2019): 397–405. Print.
APA
Cremen, M. C. M., Leliaert, F., West, J., Lam, D. W., Shimada, S., Lopez-Bautista, J. M., & Verbruggen, H. (2019). Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses. MOLECULAR PHYLOGENETICS AND EVOLUTION, 130, 397–405.
Chicago author-date
Cremen, Ma Chiela M, Frédérik Leliaert, John West, Daryl W Lam, Satoshi Shimada, Juan M Lopez-Bautista, and Heroen Verbruggen. 2019. “Reassessment of the Classification of Bryopsidales (Chlorophyta) Based on Chloroplast Phylogenomic Analyses.” Molecular Phylogenetics and Evolution 130: 397–405.
Chicago author-date (all authors)
Cremen, Ma Chiela M, Frédérik Leliaert, John West, Daryl W Lam, Satoshi Shimada, Juan M Lopez-Bautista, and Heroen Verbruggen. 2019. “Reassessment of the Classification of Bryopsidales (Chlorophyta) Based on Chloroplast Phylogenomic Analyses.” Molecular Phylogenetics and Evolution 130: 397–405.
Vancouver
1.
Cremen MCM, Leliaert F, West J, Lam DW, Shimada S, Lopez-Bautista JM, et al. Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses. MOLECULAR PHYLOGENETICS AND EVOLUTION. 2019;130:397–405.
IEEE
[1]
M. C. M. Cremen et al., “Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses,” MOLECULAR PHYLOGENETICS AND EVOLUTION, vol. 130, pp. 397–405, 2019.
@article{8606360,
  abstract     = {The Bryopsidales is a morphologically diverse group of mainly marine green macroalgae characterized by a siphonous structure. The order is composed of three suborders – Ostreobineae, Bryopsidineae, and Halimedineae. While previous studies improved the higher-level classification of the order, the taxonomic placement of some genera in Bryopsidineae (Pseudobryopsis and Lambia) as well as the relationships between the families of Halimedineae remains uncertain. In this study, we re-assess the phylogeny of the order with datasets derived from chloroplast genomes, drastically increasing the taxon sampling by sequencing 32 new chloroplast genomes. The phylogenies presented here provided good support for the major lineages (suborders and most families) in Bryopsidales. In Bryopsidineae, Pseudobryopsis hainanensis was inferred as a distinct lineage from the three established families allowing us to establish the family Pseudobryopsidaceae. The Antarctic species Lambia antarctica was shown to be an early-branching lineage in the family Bryopsidaceae. In Halimedineae, we revealed several inconsistent phylogenetic positions of macroscopic taxa, and several entirely new lineages of microscopic species. A new classification scheme is proposed, which includes the merger of the families Pseudocodiaceae, Rhipiliaceae and Udoteaceae into a more broadly circumscribed Halimedaceae, and the establishment of tribes for the different lineages found therein. In addition, the deep-water genus Johnson-sea-linkia, currently placed in Rhipiliopsis, was reinstated based on our phylogeny.},
  author       = {Cremen, Ma Chiela M and Leliaert, Frédérik and West, John and Lam, Daryl W and Shimada, Satoshi and Lopez-Bautista, Juan M and Verbruggen, Heroen},
  issn         = {1055-7903},
  journal      = {MOLECULAR PHYLOGENETICS AND EVOLUTION},
  keywords     = {Siphonous green algae,Seaweeds,Chloroplast genome,Phylogeny,Ulvophyceae,UDOTEACEAE BRYOPSIDALES,GENUS,SELECTION,HALIMEDA,GENOME,AVRAINVILLEA,ULVOPHYCEAE,DIVERSITY,ALGORITHM,ALIGNMENT},
  language     = {eng},
  pages        = {397--405},
  title        = {Reassessment of the classification of Bryopsidales (Chlorophyta) based on chloroplast phylogenomic analyses},
  url          = {http://dx.doi.org/10.1016/j.ympev.2018.09.009},
  volume       = {130},
  year         = {2019},
}

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